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Pal G, Di L, Orunmuyi A, Olapade-Olaopa EO, Qiu W, Ogunwobi OO. Population Differentiation at the PVT1 Gene Locus: Implications for Prostate Cancer. G3 (BETHESDA, MD.) 2020; 10:2257-2264. [PMID: 32358016 PMCID: PMC7341130 DOI: 10.1534/g3.120.401291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
Genetic variation in susceptibility to complex diseases, such as cancer, is well-established. Enrichment of disease associated alleles in specific populations could have implications for disease incidence and prevalence. Prostate cancer (PCa) is a disease with well-established higher incidence, prevalence, and worse outcomes among men of African ancestry in comparison to other populations. PCa is a multi-factorial, complex disease, but the exact mechanisms for its development and progression are unclear. The gene desert located on chromosome 8q24 is associated with aggressiveness of PCa. Interestingly, the non-protein coding gene locus Plasmacytoma Variant Translocation (PVT1) is present at chromosome 8q24 and is overexpressed in PCa. PVT1 gives rise to multiple transcripts with potentially different molecular and cellular functions. In an analysis of the PVT1 locus using data from the 1000 Genomes Project, we found the chromosomal region spanning PVT1 exons 4A and 4B to be highly differentiated between African and non-African populations. We further investigated levels of gene expression of PVT1 exons 4A and 4B and observed significant overexpression of these exons in PCa tissues relative to benign prostatic hyperplasia and to normal prostate tissues obtained from men of African ancestry. These results indicate that PVT1 exons 4A and 4B may have clinical implications in PCa a conclusion supported by the observation that transient and stable overexpression of PVT1 exons 4A and 4B significantly induce greater prostate epithelial cell migration and proliferation. We anticipate that further exploration of the role of PVT1 exons 4A and 4B may lead to the development of diagnostic, therapeutic, and other clinical applications in PCa.
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Affiliation(s)
- Gargi Pal
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | - Lia Di
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | | | | | - Weigang Qiu
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | - Olorunseun O Ogunwobi
- Department of Biological Sciences, Hunter College of The City University of New York, NY,
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY
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102
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Harlemon M, Ajayi O, Kachambwa P, Kim MS, Simonti CN, Quiver MH, Petersen DC, Mittal A, Fernandez PW, Hsing AW, Baichoo S, Agalliu I, Jalloh M, Gueye SM, Snyper NYF, Adusei B, Mensah JE, Abrahams AOD, Adebiyi AO, Orunmuyi AT, Aisuodionoe-Shadrach OI, Nwegbu MM, Joffe M, Chen WC, Irusen H, Neugut AI, Quintana Y, Seutloali M, Fadipe MB, Warren C, Woehrmann MH, Zhang P, Ongaco CM, Mawhinney M, McBride J, Andrews CV, Adams M, Pugh E, Rebbeck TR, Petersen LN, Lachance J. A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa. Cancer Res 2020; 80:2956-2966. [PMID: 32393663 PMCID: PMC7335354 DOI: 10.1158/0008-5472.can-19-2165] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/03/2019] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Although prostate cancer is the leading cause of cancer mortality for African men, the vast majority of known disease associations have been detected in European study cohorts. Furthermore, most genome-wide association studies have used genotyping arrays that are hindered by SNP ascertainment bias. To overcome these disparities in genomic medicine, the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network has developed a genotyping array that is optimized for African populations. The MADCaP Array contains more than 1.5 million markers and an imputation backbone that successfully tags over 94% of common genetic variants in African populations. This array also has a high density of markers in genomic regions associated with cancer susceptibility, including 8q24. We assessed the effectiveness of the MADCaP Array by genotyping 399 prostate cancer cases and 403 controls from seven urban study sites in sub-Saharan Africa. Samples from Ghana and Nigeria clustered together, whereas samples from Senegal and South Africa yielded distinct ancestry clusters. Using the MADCaP array, we identified cancer-associated loci that have large allele frequency differences across African populations. Polygenic risk scores for prostate cancer were higher in Nigeria than in Senegal. In summary, individual and population-level differences in prostate cancer risk were revealed using a novel genotyping array. SIGNIFICANCE: This study presents an Africa-specific genotyping array, which enables investigators to identify novel disease associations and to fine-map genetic loci that are associated with prostate and other cancers.
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Affiliation(s)
- Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
- Clark Atlanta University, Atlanta, Georgia
| | - Olabode Ajayi
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Corinne N Simonti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | | | - Pedro W Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Ilir Agalliu
- Albert Einstein College of Medicine, Bronx, New York
| | - Mohamed Jalloh
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | - Serigne M Gueye
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | | | | | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana, Accra, Ghana
| | | | | | | | | | - Maxwell M Nwegbu
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Maureen Joffe
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
- MRC Developmental Pathways to Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Wenlong C Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Hayley Irusen
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Yuri Quintana
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | | | - Mayowa B Fadipe
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | | | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Chrissie M Ongaco
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Michelle Mawhinney
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Jo McBride
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Marcia Adams
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.
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103
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Song L, Liu A, Shi J. SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics. Bioinformatics 2020; 35:4038-4044. [PMID: 30911754 DOI: 10.1093/bioinformatics/btz176] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/08/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Polygenic risk score (PRS) methods based on genome-wide association studies (GWAS) have a potential for predicting the risk of developing complex diseases and are expected to become more accurate with larger training datasets and innovative statistical methods. The area under the ROC curve (AUC) is often used to evaluate the performance of PRSs, which requires individual genotypic and phenotypic data in an independent GWAS validation dataset. We are motivated to develop methods for approximating AUC of PRSs based on the summary level data of the validation dataset, which will greatly facilitate the development of PRS models for complex diseases. RESULTS We develop statistical methods and an R package SummaryAUC for approximating the AUC and its variance of a PRS when only the summary level data of the validation dataset are available. SummaryAUC can be applied to PRSs with SNPs either genotyped or imputed in the validation dataset. We examined the performance of SummaryAUC using a large-scale GWAS of schizophrenia. SummaryAUC provides accurate approximations to AUCs and their variances. The bias of AUC is typically <0.5% in most analyses. SummaryAUC cannot be applied to PRSs that use all SNPs in the genome because it is computationally prohibitive. AVAILABILITY AND IMPLEMENTATION https://github.com/lsncibb/SummaryAUC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lei Song
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Aiyi Liu
- Biostatistics and Bioinformatics Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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104
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Bicak M, Wang X, Gao X, Xu X, Väänänen RM, Taimen P, Lilja H, Pettersson K, Klein RJ. Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB. Hum Mol Genet 2020; 29:1581-1591. [PMID: 32065238 PMCID: PMC7526792 DOI: 10.1093/hmg/ddaa026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/25/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
How genome-wide association studies-identified single-nucleotide polymorphisms (SNPs) affect remote genes remains unknown. Expression quantitative trait locus (eQTL) association meta-analysis on 496 prostate tumor and 602 normal prostate samples with 117 SNPs revealed novel cis-eQTLs and trans-eQTLs. Mediation testing and colocalization analysis demonstrate that MSMB is a cis-acting mediator for SNHG11 (P < 0.01). Removing rs10993994 in LNCaP cell lines by CRISPR/Cas9 editing shows that the C-allele corresponds with an over 100-fold increase in MSMB expression and 5-fold increase in SNHG11 compared with the T-allele. Colocalization analysis confirmed that the same set of SNPs associated with MSMB expression is associated with SNHG11 expression (posterior probability of shared variants is 66.6% in tumor and 91.4% in benign). These analyses further demonstrate variants driving MSMB expression differ in tumor and normal, suggesting regulatory network rewiring during tumorigenesis.
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Affiliation(s)
- Mesude Bicak
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xing Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoni Gao
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xing Xu
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Pekka Taimen
- Department of Pathology, University of Turku, 20014 Turku, and Turku University Hospital, 20521 Turku, Finland
| | - Hans Lilja
- Department of Laboratory Medicine, Surgery and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, UK
- Department of Translational Medicine, Lund University, Malmö 205 02, Sweden
| | - Kim Pettersson
- Division of Biotechnology, University of Turku, Turku, Finland
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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105
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Ahmed M, Goh C, Saunders E, Cieza-Borrella C, Kote-Jarai Z, Schumacher FR, Eeles R. Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT. Prostate Cancer Prostatic Dis 2020; 23:333-342. [PMID: 31776447 PMCID: PMC7237354 DOI: 10.1038/s41391-019-0181-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/02/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The development of prostate cancer can be influenced by genetic and environmental factors. Numerous germline SNPs influence prostate cancer susceptibility. The functional pathways in which these SNPs increase prostate cancer susceptibility are unknown. Finasteride is currently not being used routinely as a chemoprevention agent but the long term outcomes of the PCPT trial are awaited. The outcomes of the SELECT trial have not recommended the use of chemoprevention in preventing prostate cancer. This study investigated whether germline risk SNPs could be used to predict outcomes in the PCPT and SELECT trial. METHODS Genotyping was performed in European men entered into the PCPT trial (n = 2434) and SELECT (n = 4885). Next generation genotyping was performed using Affymetrix® Eureka™ Genotyping protocols. Logistic regression models were used to test the association of risk scores and the outcomes in the PCPT and SELECT trials. RESULTS Of the 100 SNPs, 98 designed successfully and genotyping was validated for samples genotyped on other platforms. A number of SNPs predicted for aggressive disease in both trials. Men with a higher polygenic score are more likely to develop prostate cancer in both trials, but the score did not predict for other outcomes in the trial. CONCLUSION Men with a higher polygenic risk score are more likely to develop prostate cancer. There were no interactions of these germline risk SNPs and the chemoprevention agents in the SELECT and PCPT trials.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK.
| | - Chee Goh
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Edward Saunders
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Clara Cieza-Borrella
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University; Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
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106
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Rashkin MD, Bowes J, Dunaway K, Dhaliwal J, Loomis E, Riffle S, Washington NL, Ziegler C, Lu J, Levin E. Genetic counseling, 2030: An on-demand service tailored to the needs of a price conscious, genetically literate, and busy world. J Genet Couns 2020; 28:456-465. [PMID: 30964579 DOI: 10.1002/jgc4.1123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
The practice of genetic counseling is going to be impacted by the public's expectation that goods, services, information, and experiences happen on demand, wherever and whenever people want them. Building from trends that are currently taking shape, this article looks just over a decade into the future-to 2030-to provide a description of how the field of genetics and genetic counseling will be changed, as well as advice for genetic counselors for how to prepare. We build from the prediction that a large portion of the general public will have access to their digitized whole genome sequence anytime, any place, on any device. We focus on five topics downstream of this prediction: public health, personal autonomy, polygenic scores (PGS), evolving clinical practices, and genetic privacy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - James Lu
- Helix Opco, LLC, San Carlos, California
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107
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Association of germline genetic variants with TMPRSS2-ERG fusion status in prostate cancer. Oncotarget 2020; 11:1321-1333. [PMID: 32341752 PMCID: PMC7170497 DOI: 10.18632/oncotarget.27534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction: Oncogenic activation of ERG resulting from TMPRSS2-ERG gene fusion is a key molecular genetic alteration in prostate cancer (CaP). The frequency of ERG fusion is variable by race; however, there are limited data available on germline polymorphisms associating with ERG fusion status. The goal of this study is to identify the inherited risk variants associating with ERG status of CaP. Materials and Methods: SNP genotyping was performed on the Illumina platform using Infinium Oncoarray SNP chip on blood derived genomic DNA samples from 400 patients treated by radical prostatectomy at a single military institution. ERG status was determined in whole mounted prostate specimens by immuno-histochemistry (IHC) for ERG protein expression. Data analysis approaches included association analyses based on EMMAX and imputation by IMPUTE2. Imputed SNPs were validated by ddPCR. Results: SNP genotyping analysis using imputation identified rs34349373 (p 4.68 × 10-8) and rs2055272 (p 5.62 × 10-8) in TBC1D22B to be significantly associated with ERG fusion status in index tumor and non-index tumor foci. Imputed SNP rs2055272 was further experimentally validated by ddPCR with 98.04% (100/102) concordance. Initial discovery analysis based on SNPs on Oncoarray SNP chip, showed significant (p 10-5) association for SNPs (rs6698333, rs1889877, rs3798999, rs10215144, rs3818136, rs9380660 and rs1792695) with ERG fusion status. The study also replicated two previously known ERG fusion associated SNPs (rs11704416 in chromsome 22; rs16901979 in chromosome 8). Conclusions: This study identified SNPs associated with ERG status of CaP. Impact: The findings may contribute towards defining the underlying genetics of ERG positive and ERG negative CaP patients.
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108
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Shu X, Long J, Cai Q, Kweon SS, Choi JY, Kubo M, Park SK, Bolla MK, Dennis J, Wang Q, Yang Y, Shi J, Guo X, Li B, Tao R, Aronson KJ, Chan KYK, Chan TL, Gao YT, Hartman M, Kee Ho W, Ito H, Iwasaki M, Iwata H, John EM, Kasuga Y, Soon Khoo U, Kim MK, Kong SY, Kurian AW, Kwong A, Lee ES, Li J, Lophatananon A, Low SK, Mariapun S, Matsuda K, Matsuo K, Muir K, Noh DY, Park B, Park MH, Shen CY, Shin MH, Spinelli JJ, Takahashi A, Tseng C, Tsugane S, Wu AH, Xiang YB, Yamaji T, Zheng Y, Milne RL, Dunning AM, Pharoah PDP, García-Closas M, Teo SH, Shu XO, Kang D, Easton DF, Simard J, Zheng W. Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants. Nat Commun 2020; 11:1217. [PMID: 32139696 PMCID: PMC7057957 DOI: 10.1038/s41467-020-15046-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
Known risk variants explain only a small proportion of breast cancer heritability, particularly in Asian women. To search for additional genetic susceptibility loci for breast cancer, here we perform a meta-analysis of data from genome-wide association studies (GWAS) conducted in Asians (24,206 cases and 24,775 controls) and European descendants (122,977 cases and 105,974 controls). We identified 31 potential novel loci with the lead variant showing an association with breast cancer risk at P < 5 × 10-8. The associations for 10 of these loci were replicated in an independent sample of 16,787 cases and 16,680 controls of Asian women (P < 0.05). In addition, we replicated the associations for 78 of the 166 known risk variants at P < 0.05 in Asians. These findings improve our understanding of breast cancer genetics and etiology and extend previous findings from studies of European descendants to Asian women.
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Affiliation(s)
- Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristan J Aronson
- Department of Public Health Sciences and Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Kelvin Y K Chan
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Department of Obstetrics & Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mikael Hartman
- Department of Surgery, National University Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Weang Kee Ho
- Department of Applied Mathematics, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center, Nagoya, Aichi, Japan
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, USA
- Departments of Health Research and Policy, School of Medicine, Stanford University, California, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, California, CA, USA
| | - Yoshio Kasuga
- Department of Surgery, Nagano Matsushiro General Hospital, Nagano, Japan
| | - Ui Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Mi-Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Hospital, National Cancer Center, Goyang, Republic of Korea
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Allison W Kurian
- Departments of Health Research and Policy, School of Medicine, Stanford University, California, CA, USA
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Surgery, University of Hong Kong, Hong Kong SAR, China
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Eun-Sook Lee
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Hospital, National Cancer Center, Goyang, Republic of Korea
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Siew-Kee Low
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Boyoung Park
- Department of Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Min-Ho Park
- Department of Surgery, Chonnam National University Medical School, Seoul, Korea
| | - Chen-Yang Shen
- College of Public Health, China Medical University, Taichong, Taiwan
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Atsushi Takahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Chiuchen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpar, Malaysia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval, Research Center, Québec City, QC, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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109
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Dai JY, Wang X, Wang B, Sun W, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Feng Z, Stanford JL. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. PLoS Genet 2020; 16:e1008667. [PMID: 32226005 PMCID: PMC7145271 DOI: 10.1371/journal.pgen.1008667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 04/09/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction. Comparing eQTLs between tumors and benign samples, we show that 98 of the 147 risk SNPs were identified as eQTLs in the tumor-adjacent benign samples, and almost all 34 eQTL identified in tumor sets were also eQTLs in the benign samples. Three lines of results support the causal role of DNA methylation. First, nearly 100 of the 147 risk SNPs were identified as meQTLs in one tumor set, and almost all eQTLs in tumors were meQTLs. Second, the loss of eQTLs in tumors relative to benign samples was associated with altered DNA methylation. Third, among risk SNPs identified as both eQTLs and meQTLs, mediation analyses suggest that over two-thirds have evidence of a causal role for DNA methylation, mostly mediating genetic influence on gene expression. In summary, we provide a comprehensive catalog of eQTLs, meQTLs and putative cancer genes for known PrCa risk SNPs. We observe that a substantial portion of germline eQTL regulatory mechanisms are maintained in the tumor development, despite somatic alterations in tumor genome. Finally, our mediation analyses illuminate the likely intermediary role of CpG methylation in eQTL regulation of gene expression.
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Affiliation(s)
- James Y. Dai
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Sun
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Kristina M. Jordahl
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Yaw A. Nyame
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Ziding Feng
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, United States of America
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110
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Huang J, Weinstein SJ, Moore SC, Derkach A, Hua X, Mondul AM, Sampson JN, Albanes D. Pre-diagnostic Serum Metabolomic Profiling of Prostate Cancer Survival. J Gerontol A Biol Sci Med Sci 2020; 74:853-859. [PMID: 29878065 DOI: 10.1093/gerona/gly128] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Indexed: 12/13/2022] Open
Abstract
Impaired metabolism may play a role in the development and lethality of prostate cancer, yet a comprehensive analysis of the interrelationships appears lacking. We measured 625 metabolites using ultrahigh performance liquid chromatography/mass spectrometry (LC-MS) and gas chromatography/mass spectrometry (GC-MS) of prediagnostic serum from 197 prostate cancer cases in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study (ages at diagnosis, 55-86 years). Cox proportional hazards models estimated associations between circulating metabolites and prostate cancer mortality for 1 SD differences (log-metabolite scale), adjusted for age, year of diagnosis, and disease stage. Associations between metabolite chemical classes and survival were examined through pathway analysis, and Cox models assessed the relationship with a sterol/steroid metabolite principal component analysis factor score. Elevated serum N-oleoyl taurine was significantly associated with prostate cancer-specific mortality (hazard ratios [HR] = 1.72 per 1 SD, p < .00008, Bonferroni-corrected threshold = 0.05/625; HR = 3.6 for highest vs lowest tertile, p < .001). Pathway analyses revealed a statistically significant association between lipids and prostate cancer death (p < .006, Bonferroni-corrected threshold = 0.05/8), and sterol/steroid metabolites showed the strongest chemical sub-class association (p = .0014, Bonferroni-corrected threshold = 0.05/45). In the principal component analysis, a 1-SD increment in the sterol/steroid metabolite score increased the risk of prostate cancer death by 46%. Prediagnostic serum N-oleoyl taurine and sterol/steroid metabolites were associated with prostate cancer survival.
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Affiliation(s)
- Jiaqi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven C Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Andriy Derkach
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Alison M Mondul
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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111
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Yuan J, Kensler KH, Hu Z, Zhang Y, Zhang T, Jiang J, Xu M, Pan Y, Long M, Montone KT, Tanyi JL, Fan Y, Zhang R, Hu X, Rebbeck TR, Zhang L. Integrative comparison of the genomic and transcriptomic landscape between prostate cancer patients of predominantly African or European genetic ancestry. PLoS Genet 2020; 16:e1008641. [PMID: 32059012 PMCID: PMC7046294 DOI: 10.1371/journal.pgen.1008641] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/27/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Men of predominantly African Ancestry (AA) have higher prostate cancer (CaP) incidence and worse survival than men of predominantly European Ancestry (EA). While socioeconomic factors drive this disparity, genomic factors may also contribute to differences in the incidence and mortality rates. To compare the prevalence of prostate tumor genomic alterations and transcriptomic profiles by patient genetic ancestry, we evaluated genomic profiles from The Cancer Genome Atlas (TCGA) CaP cohort (n = 498). Patient global and local genetic ancestry were estimated by computational algorithms using genotyping data; 414 (83.1%) were EA, 61 (12.2%) were AA, 11 (2.2%) were East Asian Ancestry (EAA), 10 (2.0%) were Native American (NA), and 2 (0.4%) were other ancestry. Genetic ancestry was highly concordant with self-identified race/ethnicity. Subsequent analyses were limited to 61 AA and 414 EA cases. Significant differences were observed by ancestry in the frequency of SPOP mutations (20.3% AA vs. 10.0% EA; p = 5.6×10-03), TMPRSS2-ERG fusions (29.3% AA vs. 39.6% EA; p = 4.4×10-02), and PTEN deletions/losses (11.5% AA vs. 30.2% EA; p = 3.5×10-03). Differentially expressed genes (DEGs) between AAs and EAs showed significant enrichment for prostate eQTL target genes (p = 8.09×10-48). Enrichment of highly expressed DEGs for immune-related pathways was observed in AAs, and for PTEN/PI3K signaling in EAs. Nearly one-third of DEGs (31.3%) were long non-coding RNAs (DE-lncRNAs). The proportion of DE-lncRNAs with higher expression in AAs greatly exceeded that with lower expression in AAs (p = 1.2×10-125). Both ChIP-seq and RNA-seq data suggested a stronger regulatory role for AR signaling pathways in DE-lncRNAs vs. non-DE-lncRNAs. CaP-related oncogenic lncRNAs, such as PVT1, PCAT1 and PCAT10/CTBP1-AS, were found to be more highly expressed in AAs. We report substantial heterogeneity in the prostate tumor genome and transcriptome between EA and AA. These differences may be biological contributors to racial disparities in CaP incidence and outcomes.
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Affiliation(s)
- Jiao Yuan
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin H. Kensler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Zhongyi Hu
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Youyou Zhang
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tianli Zhang
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Junjie Jiang
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mu Xu
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yutian Pan
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Meixiao Long
- Department of Internal Medicine, Division of Hematology, Ohio State University, Columbus, Ohio, United States of America
| | - Kathleen T. Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Janos L. Tanyi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rugang Zhang
- Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Xiaowen Hu
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Timothy R. Rebbeck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lin Zhang
- Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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112
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Fredsøe J, Koetsenruyter J, Vedsted P, Kirkegaard P, Væth M, Edwards A, Ørntoft TF, Sørensen KD, Bro F. The effect of assessing genetic risk of prostate cancer on the use of PSA tests in primary care: A cluster randomized controlled trial. PLoS Med 2020; 17:e1003033. [PMID: 32032355 PMCID: PMC7006905 DOI: 10.1371/journal.pmed.1003033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/15/2020] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Assessing genetic lifetime risk for prostate cancer has been proposed as a means of risk stratification to identify those for whom prostate-specific antigen (PSA) testing is likely to be most valuable. This project aimed to test the effect of introducing a genetic test for lifetime risk of prostate cancer in general practice on future PSA testing. METHODS AND FINDINGS We performed a cluster randomized controlled trial with randomization at the level of general practices (73 in each of two arms) in the Central Region (Region Midtjylland) of Denmark. In intervention practices, men were offered a genetic test (based on genotyping of 33 risk-associated single nucleotide polymorphisms) in addition to the standard PSA test that informed them about lifetime genetic risk of prostate cancer and distinguished between "normal" and "high" risk. The primary outcome was the proportion of men having a repeated PSA test within 2 years. A multilevel logistic regression model was used to test the association. After applying the exclusion criteria, 3,558 men were recruited in intervention practices, with 1,235 (34.7%) receiving the genetic test, and 4,242 men were recruited in control practices. Men with high genetic risk had a higher propensity for repeated PSA testing within 2 years than men with normal genetic risk (odds ratio [OR] = 8.94, p < 0.01). The study was conducted in routine practice and had some selection bias, which is evidenced by the relatively large proportion of younger and higher income participants taking the genetic test. CONCLUSIONS Providing general practitioners (GPs) with access to a genetic test to assess lifetime risk of prostate cancer did not reduce the overall number of future PSA tests. However, among men who had a genetic test, knowledge of genetic risk significantly influenced future PSA testing. TRIAL REGISTRATION This study is registered with ClinicalTrials.gov, number NCT01739062.
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Affiliation(s)
- Jacob Fredsøe
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jan Koetsenruyter
- Research Unit for General Practice, The Research Centre for Cancer Diagnosis in Primary Care (Cap), Aarhus University, Aarhus, Denmark
| | - Peter Vedsted
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Research Unit for General Practice, The Research Centre for Cancer Diagnosis in Primary Care (Cap), Aarhus University, Aarhus, Denmark
| | - Pia Kirkegaard
- Department of Public Health, Randers Regional Hospital, Randers, Denmark
| | - Michael Væth
- Department of Public Health, Section of Biostatistics, Aarhus University, Aarhus, Denmark
| | - Adrian Edwards
- Division of Population Medicine, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Torben F. Ørntoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D. Sørensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Flemming Bro
- Research Unit for General Practice, The Research Centre for Cancer Diagnosis in Primary Care (Cap), Aarhus University, Aarhus, Denmark
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113
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: https:/doi.org/10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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114
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Badal S, Aiken W, Morrison B, Valentine H, Bryan S, Gachi A, Ragin C. Disparities in prostate cancer incidence and mortality rates: Solvable or not? Prostate 2020; 80:3-16. [PMID: 31702061 PMCID: PMC8378246 DOI: 10.1002/pros.23923] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/18/2019] [Indexed: 12/21/2022]
Abstract
Prostate cancer (PCa) is recognized as a disease possessing not only great variation in its geographic and racial distribution but also tremendous variation in its potential to cause morbidity and death and it, therefore, ought not to be considered a homogenous disease entity. Morbidity and death from PCa are disproportionately higher in men of African ancestry (MAA) who are generally observed to have more aggressive disease and worse outcomes following treatment compared to men of European ancestry (MEA). The higher rates of PCa among MAA relative to MEA appear to be multifactorial and related to inherent differences in biological aggressiveness; a continued lack of awareness of the disease and methods of prevention; a lower prevalence of screen-detected PCa; comparatively lower access to quality healthcare as well as systemic and institutionalized disparities in the administration of optimal care to MAA in developed countries such as the United States of America where high-quality care is available. Even when access to quality healthcare is assured in equal access settings, it appears that MAA still have worse outcomes after PCa treatment stage-for-stage and grade-for-grade compared to MEA, suggesting that, inherent racial, ethnic and biological differences are paramount in predicting poor outcomes. This review has explored the different contributing factors to the current disparities in PCa incidence and mortality rates with emphasis on the incongruence in how research has been conducted in understanding the disease towards developing therapies.
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Affiliation(s)
- Simone Badal
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - William Aiken
- Department of Surgery, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Belinda Morrison
- Department of Surgery, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Henkel Valentine
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Sophia Bryan
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Andrew Gachi
- Department of pathology, Aga Khan University Hospital, 3 Avenue, Parklands, Nairobi, Kenya
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- African Caribbean Cancer Consortium
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115
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: 10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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116
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McCartney DL, Zhang F, Hillary RF, Zhang Q, Stevenson AJ, Walker RM, Bermingham ML, Boutin T, Morris SW, Campbell A, Murray AD, Whalley HC, Porteous DJ, Hayward C, Evans KL, Chandra T, Deary IJ, McIntosh AM, Yang J, Visscher PM, McRae AF, Marioni RE. An epigenome-wide association study of sex-specific chronological ageing. Genome Med 2019; 12:1. [PMID: 31892350 PMCID: PMC6938636 DOI: 10.1186/s13073-019-0693-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/15/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Advanced age is associated with cognitive and physical decline and is a major risk factor for a multitude of disorders. There is also a gap in life expectancy between males and females. DNA methylation differences have been shown to be associated with both age and sex. Here, we investigate age-by-sex differences in blood-based DNA methylation in an unrelated cohort of 2586 individuals between the ages of 18 and 87 years, with replication in a further 4450 individuals between the ages of 18 and 93 years. METHODS Linear regression models were applied, with stringent genome-wide significance thresholds (p < 3.6 × 10-8) used in both the discovery and replication data. A second, highly conservative mixed linear model method that better controls the false-positive rate was also applied, using the same genome-wide significance thresholds. RESULTS Using the linear regression method, 52 autosomal and 597 X-linked CpG sites, mapping to 251 unique genes, replicated with concordant effect size directions in the age-by-sex interaction analysis. The site with the greatest difference mapped to GAGE10, an X-linked gene. Here, DNA methylation levels remained stable across the male adult age range (DNA methylation by age r = 0.02) but decreased across female adult age range (DNA methylation by age r = - 0.61). One site (cg23722529) with a significant age-by-sex interaction also had a quantitative trait locus (rs17321482) that is a genome-wide significant variant for prostate cancer. The mixed linear model method identified 11 CpG sites associated with the age-by-sex interaction. CONCLUSION The majority of differences in age-associated DNA methylation trajectories between sexes are present on the X chromosome. Several of these differences occur within genes that have been implicated in sexually dimorphic traits.
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Affiliation(s)
- Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Futao Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, Scotland, UK
| | - Heather C Whalley
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, Scotland, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Tamir Chandra
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK.
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117
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Meissner VH, Bittner R, Kron M, Schiele S, Schulwitz H, Gschwend JE, Herkommer K. Impact of a Changing Population Structure and Clustering of Cancer in Prostate Cancer Patients Depending on a First-Degree Family History. Urol Int 2019; 104:222-229. [PMID: 31865349 DOI: 10.1159/000504789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/13/2019] [Indexed: 02/03/2023]
Abstract
INTRODUCTION In the last century, there have been major changes within the population structure in Germany. The aim of this study was to determine the impact of a changing population structure on identification of familial prostate cancer (PCa), and to investigate how many and which types of other cancers have occurred in patients and their first-degree relatives. MATERIALS AND METHODS A total of 19,540 patients were evaluated in a prospectively collected PCa family database and divided into four birth cohorts: 1925-1934 (cohort A), 1935-1944 (cohort B), 1945-1954 (cohort C), and 1955-1964 (cohort D). Other primary cancers and cancers of first-degree relatives were evaluated. RESULTS The percentage of PCa patients with ≥2 sons declined (A: 28.9% to D: 21.6%). The percentage of patients whose fathers lived for ≥65 years increased (B: 64.2% to D: 73.0%). Malignancies of the skin, the urinary tract, and the lymphoid/hematopoietic tissue were more common in patients with a positive first-degree PCa family history and their first-degree relatives. Additionally, first-degree relatives reported more often neoplasms of respiratory/intrathoracic organs and the female breast. CONCLUSIONS A small family size, an early deceased father, and a high number of sporadic cases complicate the identification of familial PCa patients. Thus, a detailed family history should also include unaffected first-degree relatives to avoid any misclassification. Findings of other primary cancers in patients and their relatives warrant further investigation.
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Affiliation(s)
- Valentin Henri Meissner
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Robert Bittner
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Martina Kron
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Stefan Schiele
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Helga Schulwitz
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Jürgen Erich Gschwend
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Kathleen Herkommer
- Department of Urology, Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany,
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118
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An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer. Sci Rep 2019; 9:17173. [PMID: 31748686 PMCID: PMC6868235 DOI: 10.1038/s41598-019-53445-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 10/25/2019] [Indexed: 01/26/2023] Open
Abstract
Since prostate cancer is highly heritable, common variants associated with prostate cancer have been studied in various populations, including those in Korea. However, rare and low-frequency variants have a significant influence on the heritability of the disease. The contributions of rare variants to prostate cancer susceptibility have not yet been systematically evaluated in a Korean population. In this work, we present a large-scale exome-wide rare variant analysis of 7,258 individuals (985 cases with prostate cancer and 6,273 controls). In total, 19 rare variant loci spanning 7 genes contributed to an association with prostate cancer susceptibility. In addition to replicating previously known susceptibility genes (e.g., CDYL2, MST1R, GPER1, and PARD3B), 3 novel genes were identified (FDR q < 0.05), including the non-coding RNAs ENTPD3-AS1, LOC102724438, and protein-coding gene SPATA3. Additionally, 6 pathways were identified based on identified variants and genes, including estrogen signaling pathway, signaling by MST1, IL-15 production, MSP-RON signaling pathway, and IL-12 signaling and production in macrophages, which are known to be associated with prostate cancer. In summary, we report novel genes and rare variants that potentially play a role in prostate cancer susceptibility in the Korean population. These observations demonstrated a path towards one of the fundamental goals of precision medicine, which is to identify biomarkers for a subset of the population with a greater risk of disease than others.
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119
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Liu WJ, Zhao G, Zhang CY, Yang CQ, Zeng XB, Li J, Zhu K, Zhao SQ, Lu HM, Yin DC, Lin SX. Comparison of the roles of estrogens and androgens in breast cancer and prostate cancer. J Cell Biochem 2019; 121:2756-2769. [PMID: 31693255 DOI: 10.1002/jcb.29515] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/10/2019] [Indexed: 12/29/2022]
Abstract
Breast cancer (BC) and prostate cancer (PC) are the second most common malignant tumors in women and men in western countries, respectively. The risks of death are 14% for BC and 9% for PC. Abnormal estrogen and androgen levels are related to carcinogenesis of the breast and prostate. Estradiol stimulates cancer development in BC. The effect of estrogen on PC is concentration-dependent, and estrogen can regulate androgen production, further affecting PC. Estrogen can also increase the risk of androgen-induced PC. Androgen has dual effects on BC via different metabolic pathways, and the role of the androgen receptor (AR) in BC also depends on cell subtype and downstream target genes. Androgen and AR can stimulate both primary PC and castration-resistant PC. Understanding the mechanisms of the effects of estrogen and androgen on BC and PC may help us to improve curative BC and PC treatment strategies.
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Affiliation(s)
- Wen-Jing Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Gang Zhao
- Breast Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Chang-Qing Yang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiang-Bin Zeng
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Jin Li
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Kun Zhu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Shi-Qi Zhao
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Hui-Meng Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Sheng-Xiang Lin
- Department of Molecular Medicine, Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL), Laval University, Québec, Canada
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120
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Ali S, Zhang Y, Zhou M, Li H, Jin W, Zheng L, Yu X, Stark JM, Weitzel JN, Shen B. Functional deficiency of DNA repair gene EXO5 results in androgen-induced genomic instability and prostate tumorigenesis. Oncogene 2019; 39:1246-1259. [PMID: 31616062 DOI: 10.1038/s41388-019-1061-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/16/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Germline mutations of DNA double-strand break (DSB) response and repair genes that drive tumorigenesis could be a major cause of prostate cancer (PCa) heritability. In this study, we demonstrated the role of novel exonuclease 5 (EXO5) gene in androgen-induced double strand breaks repair via homology-directed repair pathway and prostate tumorigenesis. Using whole-exome sequencing of samples from 20 PCa families, with three or more siblings diagnosed with metastatic PCa, we identified mutations in 31 genes involved in DSB response and repair. Among them, the L151P mutation in the exonuclease 5 (EXO5) gene was present in all affected siblings in three PCa families. We found two other EXO5 SNPs significantly associated with risk of PCa in cases-controls study from databases of genotype and phenotype (dbGaP), which are in linkage disequilibrium (D' = 1) with Exo5 L151P found in PCa family. The L151 residue is conserved across diverse species and its mutation is deleterious for protein functions, as demonstrated by our bioinformatics analyses. The L151P mutation impairs the DNA repair function of EXO5 due to loss of nuclease activity, as well as failure of nuclear localization. CRISPR elimination of EXO5 in a PCa cell line impaired homology-directed recombination repair (HDR) and caused androgen-induced genomic instability, as indicated by frequent occurrence of the oncogenic fusion transcript TMPRSS2-ERG. Genetic and functional validation of the EXO5 mutations indicated that EXO5 is a risk gene for prostate tumorigenesis, likely due to its functions in HDR.
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Affiliation(s)
- Shafat Ali
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Yilan Zhang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, USA
| | - Weiwei Jin
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Jeffrey N Weitzel
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA.
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Christophersen MK, Høgdall C, Høgdall E. The prospect of discovering new biomarkers for ovarian cancer based on current knowledge of susceptibility loci and genetic variation (Review). Int J Mol Med 2019; 44:1599-1608. [PMID: 31573049 DOI: 10.3892/ijmm.2019.4352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/30/2019] [Indexed: 11/05/2022] Open
Abstract
Ovarian cancer is the most lethal gynaecological malignancy. The cancer initially presents with non‑specific symptoms; thus, it is typically not discovered until the patient has reached the late, considerably more lethal, stages of the disease. Research focus is currently on finding novel biomarkers, especially for early detection and stratification of the disease. One promising approach has been to focus on mutations or variations in the genetic code that are associated with the risk of developing ovarian cancer. A certain heritable component is already known regarding genes such as BRCA1/2, TP53, MSH6, BRIP1 and RAD51C, yet these are estimated to only account for ~3.1% of the total risk. Recent advances in sequencing technologies have enabled the investigation of hundreds of thousands of genetic variants in genome‑wide association studies in tens of thousands of patients, which has led to the discovery of 108 (39 loci with P<5.0x10‑8) novel susceptibility loci for ovarian cancer, presented in this review. Using the published variants in a patient cohort screening, together with variants identified in our ongoing whole exome sequencing project, future aims are to ascertain whether certain of the novel variants could be used as biomarkers for early diagnosis and/or treatment decisions.
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Affiliation(s)
- Mikael Kronborg Christophersen
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Claus Høgdall
- The Juliane Marie Centre, Department of Gynaecology, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
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122
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12 new susceptibility loci for prostate cancer identified by genome-wide association study in Japanese population. Nat Commun 2019; 10:4422. [PMID: 31562322 PMCID: PMC6764957 DOI: 10.1038/s41467-019-12267-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/02/2019] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified ~170 genetic loci associated with prostate cancer (PCa) risk, but most of them were identified in European populations. We here performed a GWAS and replication study using a large Japanese cohort (9,906 cases and 83,943 male controls) to identify novel susceptibility loci associated with PCa risk. We found 12 novel loci for PCa including rs1125927 (TMEM17, P = 3.95 × 10−16), rs73862213 (GATA2, P = 5.87 × 10−23), rs77911174 (ZMIZ1, P = 5.28 × 10−20), and rs138708 (SUN2, P = 1.13 × 10−15), seven of which had crucially low minor allele frequency in European population. Furthermore, we stratified the polygenic risk for Japanese PCa patients by using 82 SNPs, which were significantly associated with Japanese PCa risk in our study, and found that early onset cases and cases with family history of PCa were enriched in the genetically high-risk population. Our study provides important insight into genetic mechanisms of PCa and facilitates PCa risk stratification in Japanese population. More than 170 genetic loci have been linked to prostate cancer risk, primarily based on genome-wide association studies (GWAS) in European population. Here, the authors performed a GWAS on a Japanese cohort of prostate cancer patients, finding 12 new susceptibility loci, and identifying a polygenic risk for Japanese prostate cancer.
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123
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Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun 2019; 10:4154. [PMID: 31515496 PMCID: PMC6742760 DOI: 10.1038/s41467-019-12079-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/15/2019] [Indexed: 12/27/2022] Open
Abstract
To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation. In prostate cancer, chromatin structure can impact the transcriptome. Here, the authors develop high resolution chromatin interaction maps in prostate cancer cells using in situ Hi-C, revealing prostate cancer-specific TADs and enhancer-promoter loops surrounding the androgen receptor (AR) locus.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fides D Lay
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jiani Shi
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jenevieve Polin
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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124
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Sargazi S, Saravani R, Zavar Reza J, Zarei Jaliani H, Galavi H, Moudi M, Alsadat Abtahi N. Novel Poly(Adenosine Diphosphate-Ribose) Polymerase (PARP) Inhibitor, AZD2461, Down-Regulates VEGF and Induces Apoptosis in Prostate Cancer Cells. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 31102368 PMCID: PMC6661129 DOI: 10.29252/.23.5.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Background Prostate cancer (Pca) is a heterogeneous disease, and current treatments are not based on molecular stratification. Poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors have recently been found to be remarkably toxic to cells with defects in homologous recombination, particularly cells with BRCA-mutated backgrounds. Therefore, this preliminary study was designed to evaluate whether PTEN expression status could have an impact on the sensitivity of invasive Pca cells to the PARP inhibitor, AZD2461. Methods MTT viability test, Annexin V‐FITC/propidium iodide double staining, and caspase3 activity assay were used to evaluate the apoptosis and relative expression of PTEN and VEGF in PC-3 and DU145 cell lines using real-time PCR. Results MTT results showed that the inhibitory effects of AZD2461 were higher in PC-3 than DU145 cells (with IC50 of 36.48 and 59.03 µM at 48 hours of treatment, respectively). Flow cytometric analysis also showed the same results. When exposed to 40 µM of AZD2461, PC-3 (38.8%) and DU145 (28%) cells underwent apoptosis (p < 0.05). Treatment of cells by AZD2461 also caused a significant increase in apoptosis through caspase3 activation in both cell lines. VEGF mRNA levels in PC-3 cells significantly decreased compared to adjusted untreated cells (p < 0.05) in all measured times while displaying different alteration patterns in DU145 cells (p < 0.05). Conclusion AZD2461 suppresses the growth of prostate tumor cells since AZD2461 monotherapy could prove to be efficacious, especially against cells not expressing PTEN besides activating the possible apoptosis-independent cell death pathways.
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Affiliation(s)
- Saman Sargazi
- International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran;,Biotechnology Research Center, International Campus, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Ramin Saravani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran;,Cellular and Molecular Research Center of Zahedan University of Medical Sciences, Zahedan, Iran;,Corresponding Authors: Ramin Saravani , Cellular and Molecular Research Center and Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran; Mobile: (+98-915) 5432609; E-mail: . Javad Zavar Reza, Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran; Mobile.: (+98-912) 5028742; E-mail:
| | - Javad Zavar Reza
- Biotechnology Research Center, International Campus, Shahid Sadoughi University of Medical Science, Yazd, Iran;,Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran;,Corresponding Authors: Ramin Saravani , Cellular and Molecular Research Center and Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran; Mobile: (+98-915) 5432609; E-mail: . Javad Zavar Reza, Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran; Mobile.: (+98-912) 5028742; E-mail:
| | - Hossein Zarei Jaliani
- Protein Engineering Laboratory, Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamidreza Galavi
- Cellular and Molecular Research Center of Zahedan University of Medical Sciences, Zahedan, Iran;,Clinical Immunology Research Center of Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Moudi
- Genetics of Non-Communicable Disease Research Center of Zahedan University of Medical Sciences, Zahedan, Iran
| | - Najmeh Alsadat Abtahi
- International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran;,Biotechnology Research Center, International Campus, Shahid Sadoughi University of Medical Science, Yazd, Iran
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Sargazi S, Saravani R, Zavar Reza J, Jaliani HZ, Mirinejad S, Rezaei Z, Zarei S. Induction of apoptosis and modulation of homologous recombination DNA repair pathway in prostate cancer cells by the combination of AZD2461 and valproic acid. EXCLI JOURNAL 2019; 18:485-498. [PMID: 31423128 PMCID: PMC6694702 DOI: 10.17179/excli2019-1098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/01/2019] [Indexed: 01/01/2023]
Abstract
Cancer therapies using defects in homologous recombination (HR) DNA repair pathway of tumor cells are not yet approved to be applicable in patients with malignancies other than BRCA1/2-mutated tumors. This study was designed to determine the efficacy of combination therapy of a histone deacetylase inhibitor, valproic acid (VPA) and a novel PARP inhibitor AZD2461 in both PC-3 (PTEN-mutated) and DU145 (PTEN-unmutated) prostate cancer cell lines. The Trypan blue dye exclusion assay and the tetrazolium-based colorimetric (MTT) assay were performed to measure the cytotoxicity while combination effects were assessed based on Chou-Talalay's principles. Flow-cytometric assay determined the type of cell death. The real-time PCR analysis was used to evaluate the alterations in mRNA levels of HR-related genes while their protein levels were measured using the ELISA method. γ-H2AX levels were determined as a marker of DNA damage. We observed a synergistic relationship between VPA and AZD2461 in all affected fractions of PC-3 cells (CI<0.9), but not in DU145 cells (CI>1.1). Annexin-V staining analysis revealed a significant induction of apoptosis when PC-3 cells were treated with VPA+AZD2461 (p<0.05). Both mRNA and protein levels of Rad51 and Mre11 were significantly decreased in PC-3 cells co-treated with VPA+AZD2461 while enhanced H2AX phosphorylation was found in PC-3 cells after 12 and 24 hours of co-treatment (p<0.05). Our findings established a preclinical rationale for selective targeting of HR repair pathways by a combination of VPA and AZD2461 as a mechanism for reducing the HR pathway sufficiency in PTEN-mutated prostate cancer cells.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Javad Zavar Reza
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Zarei Jaliani
- Protein Engineering Laboratory, Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zohreh Rezaei
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran
| | - Sadegh Zarei
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Stelcer E, Konkol M, Głȩboka A, Suchorska WM. Liquid Biopsy in Oligometastatic Prostate Cancer-A Biologist's Point of View. Front Oncol 2019; 9:775. [PMID: 31475117 PMCID: PMC6702517 DOI: 10.3389/fonc.2019.00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the main cause of cancer-related mortality in males and the diagnosis, treatment, and care of these patients places a great burden on healthcare systems globally. Clinically, PCa is highly heterogeneous, ranging from indolent tumors to highly aggressive disease. In many cases treatment-generally either radiotherapy (RT) or surgery-can be curative. Several key genetic and demographic factors such as age, family history, genetic susceptibility, and race are associated with a high incidence of PCa. While our understanding of PCa, which is mainly based on the tools of molecular biology-has improved dramatically in recent years, efforts to better understand this complex disease have led to the identification of a new type of PCa-oligometastatic PCa. Oligometastatic disease should be considered an individual, heterogeneous entity with distinct metastatic phenotypes and, consequently, wide prognostic variability. In general, patients with oligometastatic disease typically present less biologically aggressive tumors whose metastatic potential is more limited and which are slow-growing. These patients are good candidates for more aggressive treatment approaches. The main aim of the presented review was to evaluate the utility of liquid biopsy for diagnostic purposes in PCa and for use in monitoring disease progression and treatment response, particularly in patients with oligometastatic PCa. Liquid biopsies offer a rapid, non-invasive approach whose use t is expected to play an important role in routine clinical practice to benefit patients. However, more research is needed to resolve the many existing discrepancies with regard to the definition and isolation method for specific biomarkers, as well as the need to determine the most appropriate markers. Consequently, the current priority in this field is to standardize liquid biopsy-based techniques. This review will help to improve understanding of the biology of PCa, particularly the recently defined condition known as "oligometastatic PCa". The presented review of the body of evidence suggests that additional research in molecular biology may help to establish novel treatments for oligometastatic PCa. In the near future, the treatment of PCa will require an interdisciplinary approach involving active cooperation among clinicians, physicians, and biologists.
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Affiliation(s)
- Ewelina Stelcer
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Konkol
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Radiation Oncology Department, Greater Poland Cancer Centre, Poznan, Poland
| | | | - Wiktoria Maria Suchorska
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
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Zhong C, Cozen W, Bolanos R, Song J, Wang SS. The role of HLA variation in lymphoma aetiology and survival. J Intern Med 2019; 286:154-180. [PMID: 31155783 DOI: 10.1111/joim.12911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epidemiologic and laboratory evidence has consistently supported a strong inflammatory and immune component for lymphoma aetiology. These studies have consistently implicated variation in the immune gene, human leucocyte antigen (HLA), to be associated with lymphoma risk. In this review, we summarize the historical and recent evidence of HLA in both lymphoma aetiology and survival. The recent momentum in uncovering HLA associations has been propelled by the conduct of genome-wide association studies (GWAS), which has permitted the evaluation of imputed HLA alleles in much larger sample sizes than historically feasible with allelotyping studies. Based on the culmination of smaller HLA typing studies and larger GWAS, we now recognize several HLA associations with Hodgkin (HL) and non-Hodgkin lymphomas (NHLs) and their subtypes. Although other genetic variants have also been implicated with lymphoma risk, it is notable that HLA associations have been reported in every NHL and HL subtype evaluated to date. Both HLA class I and class II alleles have been linked with NHL and HL risk. It is notable that the associations identified are largely specific to each lymphoma subtype. However, pleiotropic HLA associations have also been observed. For example, rs10484561, which is in linkage disequilibrium with HLA-DRB1*01:01˜DQA1*01:01˜DQB1*05:01, has been implicated in increased FL and DLBCL risk. Opposing HLA associations across subtypes have also been reported, such as for HLA-A*01:01 which is associated with increased risk of EBV-positive cHL but decreased risk of EBV-negative cHL and chronic lymphocytic leukaemia/small cell lymphoma. Due to extensive linkage disequilibrium and allele/haplotypic variation across race/ethnicities, identification of causal alleles/haplotypes remains challenging. Follow-up functional studies are needed to identify the specific immunological pathways responsible in the multifactorial aetiology of HL and NHL. Correlative studies linking HLA alleles with known molecular subtypes and HLA expression in the tumours are also needed. Finally, additional association studies investigating HLA diversity and lymphoma survival are also required to replicate initial associations reported to date.
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Affiliation(s)
- C Zhong
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute and Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - W Cozen
- Genetic Epidemiology Center, Department of Preventive Medicine, Keck School of Medicine of USC, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - R Bolanos
- Genetic Epidemiology Center, Department of Preventive Medicine, Keck School of Medicine of USC, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - J Song
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - S S Wang
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute and Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
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128
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Rogez B, Würthner L, Petrova AB, Zierhut FB, Saczko-Brack D, Huergo MA, Batters C, Frey E, Veigel C. Reconstitution reveals how myosin-VI self-organises to generate a dynamic mechanism of membrane sculpting. Nat Commun 2019; 10:3305. [PMID: 31341165 PMCID: PMC6656732 DOI: 10.1038/s41467-019-11268-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/24/2019] [Indexed: 01/24/2023] Open
Abstract
One enigma in biology is the generation, sensing and maintenance of membrane curvature. Curvature-mediating proteins have been shown to induce specific membrane shapes by direct insertion and nanoscopic scaffolding, while the cytoskeletal motors exert forces indirectly through microtubule and actin networks. It remains unclear, whether the manifold direct motorprotein-lipid interactions themselves constitute another fundamental route to remodel the membrane shape. Here we show, combining super-resolution-fluorescence microscopy and membrane-reshaping nanoparticles, that curvature-dependent lipid interactions of myosin-VI on its own, remarkably remodel the membrane geometry into dynamic spatial patterns on the nano- to micrometer scale. We propose a quantitative theoretical model that explains this dynamic membrane sculpting mechanism. The emerging route of motorprotein-lipid interactions reshaping membrane morphology by a mechanism of feedback and instability opens up hitherto unexplored avenues of membrane remodelling and links cytoskeletal motors to early events in the sequence of membrane sculpting in eukaryotic cell biology.
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Affiliation(s)
- Benoit Rogez
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
| | - Laeschkir Würthner
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
- Arnold-Sommerfeld-Center for Theoretical Physics (ASC), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333, München, Germany
| | - Anastasiia B Petrova
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
| | - Felix B Zierhut
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
| | - Dario Saczko-Brack
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
| | - Maria-Ana Huergo
- Theoretical and Applied Physical Chemistry Research Institute (INIFTA), National University of La Plata, Diagonal 113, 1900, La Plata, Argentina
| | - Christopher Batters
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany
| | - Erwin Frey
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany.
- Arnold-Sommerfeld-Center for Theoretical Physics (ASC), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333, München, Germany.
| | - Claudia Veigel
- Department of Cellular Physiology, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Grosshadernerstrasse 9, 82152, Planegg-Martinsried, Germany.
- Center for Nanosciences (CeNS), Ludwig-Maximilians-Universität München, Schellingstrasse 4, 80799, München, Germany.
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129
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Pulley JM, Rhoads JP, Jerome RN, Challa AP, Erreger KB, Joly MM, Lavieri RR, Perry KE, Zaleski NM, Shirey-Rice JK, Aronoff DM. Using What We Already Have: Uncovering New Drug Repurposing Strategies in Existing Omics Data. Annu Rev Pharmacol Toxicol 2019; 60:333-352. [PMID: 31337270 DOI: 10.1146/annurev-pharmtox-010919-023537] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The promise of drug repurposing is to accelerate the translation of knowledge to treatment of human disease, bypassing common challenges associated with drug development to be more time- and cost-efficient. Repurposing has an increased chance of success due to the previous validation of drug safety and allows for the incorporation of omics. Hypothesis-generating omics processes inform drug repurposing decision-making methods on drug efficacy and toxicity. This review summarizes drug repurposing strategies and methodologies in the context of the following omics fields: genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, phenomics, pregomics, and personomics. While each omics field has specific strengths and limitations, incorporating omics into the drug repurposing landscape is integral to its success.
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Affiliation(s)
- Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jillian P Rhoads
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Anup P Challa
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kevin B Erreger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Meghan M Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Robert R Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kelly E Perry
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Nicole M Zaleski
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - David M Aronoff
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.,Departments of Obstetrics and Gynecology, and Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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130
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Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun 2019; 10:3107. [PMID: 31308362 PMCID: PMC6629701 DOI: 10.1038/s41467-019-10808-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/04/2019] [Indexed: 12/16/2022] Open
Abstract
Here we train cis-regulatory models of prostate tissue gene expression and impute expression transcriptome-wide for 233,955 European ancestry men (14,616 prostate cancer (PrCa) cases, 219,339 controls) from two large cohorts. Among 12,014 genes evaluated in the UK Biobank, we identify 38 associated with PrCa, many replicating in the Kaiser Permanente RPGEH. We report the association of elevated TMPRSS2 expression with increased PrCa risk (independent of a previously-reported risk variant) and with increased tumoral expression of the TMPRSS2:ERG fusion-oncogene in The Cancer Genome Atlas, suggesting a novel germline-somatic interaction mechanism. Three novel genes, HOXA4, KLK1, and TIMM23, additionally replicate in the RPGEH cohort. Furthermore, 4 genes, MSMB, NCOA4, PCAT1, and PPP1R14A, are associated with PrCa in a trans-ethnic meta-analysis (N = 9117). Many genes exhibit evidence for allele-specific transcriptional activation by PrCa master-regulators (including androgen receptor) in Position Weight Matrix, Chip-Seq, and Hi-C experimental data, suggesting common regulatory mechanisms for the associated genes.
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131
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de Jonge JJ, Batters C, O'Loughlin T, Arden SD, Buss F. The MYO6 interactome: selective motor-cargo complexes for diverse cellular processes. FEBS Lett 2019; 593:1494-1507. [PMID: 31206648 DOI: 10.1002/1873-3468.13486] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Myosins of class VI (MYO6) are unique actin-based motor proteins that move cargo towards the minus ends of actin filaments. As the sole myosin with this directionality, it is critically important in a number of biological processes. Indeed, loss or overexpression of MYO6 in humans is linked to a variety of pathologies including deafness, cardiomyopathy, neurodegenerative diseases as well as cancer. This myosin interacts with a wide variety of direct binding partners such as for example the selective autophagy receptors optineurin, TAX1BP1 and NDP52 and also Dab2, GIPC, TOM1 and LMTK2, which mediate distinct functions of different MYO6 isoforms along the endocytic pathway. Functional proteomics has recently been used to identify the wider MYO6 interactome including several large functionally distinct multi-protein complexes, which highlight the importance of this myosin in regulating the actin and septin cytoskeleton. Interestingly, adaptor-binding not only triggers cargo attachment, but also controls the inactive folded conformation and dimerisation of MYO6. Thus, the C-terminal tail domain mediates cargo recognition and binding, but is also crucial for modulating motor activity and regulating cytoskeletal track dynamics.
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Affiliation(s)
| | | | - Thomas O'Loughlin
- Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Susan D Arden
- Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, UK
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132
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Du Z, Hopp H, Ingles SA, Huff C, Sheng X, Weaver B, Stern M, Hoffmann TJ, John EM, Van Den Eeden SK, Strom S, Leach RJ, Thompson IM, Witte JS, Conti DV, Haiman CA. A genome-wide association study of prostate cancer in Latinos. Int J Cancer 2019; 146:1819-1826. [PMID: 31226226 PMCID: PMC7028127 DOI: 10.1002/ijc.32525] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022]
Abstract
Latinos represent <1% of samples analyzed to date in genome‐wide association studies of cancer. The clinical value of genetic information in guiding personalized medicine in populations of non‐European ancestry will require additional discovery and risk locus characterization efforts across populations. In the present study, we performed a GWAS of prostate cancer (PrCa) in 2,820 Latino PrCa cases and 5,293 controls to search for novel PrCa risk loci and to examine the generalizability of known PrCa risk loci in Latino men. We also conducted a genetic admixture‐mapping scan to identify PrCa risk alleles associated with local ancestry. Genome‐wide significant associations were observed with 84 variants all located at the known PrCa risk regions at 8q24 (128.484–128.548) and 10q11.22 (MSMB gene). In admixture mapping, we observed genome‐wide significant associations with local African ancestry at 8q24. Of the 162 established PrCa risk variants that are common in Latino men, 135 (83.3%) had effects that were directionally consistent as previously reported, among which 55 (34.0%) were statistically significant with p < 0.05. A polygenic risk model of the known PrCa risk variants showed that, compared to men with average risk (25th–75th percentile of the polygenic risk score distribution), men in the top 10% had a 3.19‐fold (95% CI: 2.65, 3.84) increased PrCa risk. In conclusion, we found that the known PrCa risk variants can effectively stratify PrCa risk in Latino men. Larger studies in Latino populations will be required to discover and characterize genetic risk variants for PrCa and improve risk stratification for this population. What's new? There is strong evidence for a genetic predisposition to prostate cancer (PrCa). Most of this information has come from European ancestry populations, with Latinos representing less than 1% of samples in cancer genome‐wide association studies (GWAS). In this study, the majority of established PrCa risk variants (83.3%) were consistently associated with PrCa risk in Latinos. A polygenic risk score comprised of GWAS‐identified risk variants could identify 10% of Latino men with a ~three‐fold increase in PrCa risk. These findings suggest that common germline variants for PrCa can stratify risk in Latino men, which has implications for targeted screening and prevention.
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Affiliation(s)
- Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Hannah Hopp
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Chad Huff
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xin Sheng
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Brandi Weaver
- Department of Urology, University of Texas Health Science Center, San Antonio, TX
| | - Mariana Stern
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Esther M John
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA.,Department of Urology, University of California San Francisco, San Francisco, CA
| | - Sara Strom
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Robin J Leach
- Department of Urology, University of Texas Health Science Center, San Antonio, TX
| | - Ian M Thompson
- Department of Urology, University of Texas Health Science Center, San Antonio, TX
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA.,Department of Urology, University of California San Francisco, San Francisco, CA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA.,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA.,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
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133
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Yu H, Shi Z, Wu Y, Wang CH, Lin X, Perschon C, Isaacs WB, Helfand BT, Lilly Zheng S, Duggan D, Mo Z, Lu D, Xu J. Concept and benchmarks for assessing narrow-sense validity of genetic risk score values. Prostate 2019; 79:1099-1105. [PMID: 31037745 DOI: 10.1002/pros.23821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND While higher genetic risk score (GRS) has been statistically associated with increased disease risk (broad-sense validity), the concept and tools for assessing the validity of reported GRS values from tests (narrow-sense validity) are underdeveloped. METHODS We propose two benchmarks for assessing the narrow-sense validity of GRS. The baseline benchmark requires that the mean GRS value in a general population approximates 1.0. The calibration benchmark assesses the agreement between observed risks and estimated risks (GRS values). We assessed benchmark performance for three prostate cancer (PCa) GRS tests, derived from three SNP panels with increasing stringency of selection criteria, in a PCa chemoprevention trial where 714 of 3225 men were diagnosed with PCa during the 4-year follow-up. RESULTS GRS from Panels 1, 2, and 3 were all statistically associated with PCa risk; P = 5.58 × 10-3 , P = 1 × 10-3 , and P = 1.5 × 10-13 , respectively (broad-sense validity). For narrow-sense validity, the mean GRS value among men without PCa was 1.33, 1.09, and 0.98 for Panels 1, 2, and 3, respectively (baseline benchmark). For assessing the calibration benchmark, observed risks were calculated for seven groups of men with GRS values <0.3, 0.3-0.79, 0.8-1.19, 1.2-1.49, 1.5-1.99, 2-2.99, and ≥3. The calibration slope (higher is better) was 0.15, 0.12, and 0.60, and the bias score (lower is better) between the observed risks and GRS values was 0.08, 0.08, and 0.02 for Panels 1, 2, and 3, respectively. CONCLUSION Performance differed considerably among GRS tests. We recommend that all GRS tests be evaluated using the two benchmarks before clinical implementation for individual risk assessment.
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Affiliation(s)
- Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Yishuo Wu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chi-Hsiung Wang
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Xiaoling Lin
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - William B Isaacs
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - David Duggan
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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134
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Wu L, Wang J, Cai Q, Cavazos TB, Emami NC, Long J, Shu XO, Lu Y, Guo X, Bauer JA, Pasaniuc B, Penney KL, Freedman ML, Kote-Jarai Z, Witte JS, Haiman CA, Eeles RA, Zheng W. Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants. Cancer Res 2019; 79:3192-3204. [PMID: 31101764 PMCID: PMC6606384 DOI: 10.1158/0008-5472.can-18-3536] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/04/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022]
Abstract
Genome-wide association study-identified prostate cancer risk variants explain only a relatively small fraction of its familial relative risk, and the genes responsible for many of these identified associations remain unknown. To discover novel prostate cancer genetic loci and possible causal genes at previously identified risk loci, we performed a transcriptome-wide association study in 79,194 cases and 61,112 controls of European ancestry. Using data from the Genotype-Tissue Expression Project, we established genetic models to predict gene expression across the transcriptome for both prostate models and cross-tissue models and evaluated model performance using two independent datasets. We identified significant associations for 137 genes at P < 2.61 × 10-6, a Bonferroni-corrected threshold, including nine genes that remained significant at P < 2.61 × 10-6 after adjusting for all known prostate cancer risk variants in nearby regions. Of the 128 remaining associated genes, 94 have not yet been reported as potential target genes at known loci. We silenced 14 genes and many showed a consistent effect on viability and colony-forming efficiency in three cell lines. Our study provides substantial new information to advance our understanding of prostate cancer genetics and biology. SIGNIFICANCE: This study identifies novel prostate cancer genetic loci and possible causal genes, advancing our understanding of the molecular mechanisms that drive prostate cancer.
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Affiliation(s)
- Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Jifeng Wang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Urology, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
| | - Nima C Emami
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joshua A Bauer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt Institute of Chemical Biology, High-Throughput Screening Facility, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - John S Witte
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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135
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Qian Y, Zhang L, Cai M, Li H, Xu H, Yang H, Zhao Z, Rhie SK, Farnham PJ, Shi J, Lu W. The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression. SCIENCE ADVANCES 2019; 5:eaaw6710. [PMID: 31328168 PMCID: PMC6636982 DOI: 10.1126/sciadv.aaw6710] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/11/2019] [Indexed: 05/15/2023]
Abstract
Genome-wide association studies identified single-nucleotide polymorphism (SNP) rs55958994 as a significant variant associated with increased susceptibility to prostate cancer. However, the mechanisms by which this SNP mediates increased risk to cancer are still unknown. In this study, we show that this variant is located in an enhancer active in prostate cancer cells. Deletion of this enhancer from prostate tumor cells resulted in decreased tumor initiation, tumor growth, and invasive migration, as well as a loss of stem-like cells. Using a combination of capture chromosome conformation capture (Capture-C) and RNA sequencing, we identified genes on the same and different chromosomes as targets regulated by the enhancer. Furthermore, we show that expression of individual candidate target genes in an enhancer-deleted cell line rescued different aspects of tumorigenesis. Our data suggest that the rs55958994-associated enhancer affects prostate cancer progression by influencing expression of multiple genes via long-range chromatin interactions.
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Affiliation(s)
- Yuyang Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Mingyang Cai
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Hongxia Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Heming Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Hongzhen Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wange Lu
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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136
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Muhammad T, Sakhawat A, Khan AA, Ma L, Gjerset RA, Huang Y. Mesenchymal stem cell-mediated delivery of therapeutic adenoviral vectors to prostate cancer. Stem Cell Res Ther 2019; 10:190. [PMID: 31238944 PMCID: PMC6593580 DOI: 10.1186/s13287-019-1268-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 01/04/2023] Open
Abstract
Background There is an urgent need for targeted biological therapies for prostate cancer with greater efficacy and less toxicity, particularly for metastatic disease, where current therapies are not curative. Therapeutic adenoviral vectors or oncolytic adenoviruses offer the possibility of a competent, nontoxic therapeutic alternative for prostate cancer. However, free viral particles must be delivered locally, an approach that does not address metastatic disease, and they display poor tumor penetration. To fully exploit the potential of these vectors, we must develop methods that improve intratumoral dissemination and allow for systemic delivery. This study establishes a proof-of-principle rationale for a novel human mesenchymal stem (stromal) cell-based approach to improving vector delivery to tumors. Methods/results We have generated mesenchymal stem cell-derived packaging cells for adenoviruses (E1-modified mesenchymal stem cells) by modifying human mesenchymal stem cells with the adenovirus (type C) E1A/B genes needed for viral replication. Using cell-based assays, we have demonstrated that two adenoviral vectors, replication-defective adenovirus expressing p14 and p53 or conditionally replicating oncolytic adenovirus, packaged by E1A/B-modified mesenchymal stem cells, suppress the growth of prostate cancer cells in culture. Using subcutaneous xenograft models for human prostate cancer in mice, we have shown that E1A/B-modified mesenchymal stem cells display tumor tropism in tumor-bearing nude mice, that E1A/B-modified mesenchymal stem cells disseminate well within tumors, and that replication-defective adenovirus expressing p14 and p53 or conditionally replicating oncolytic adenovirus-loaded E1-modified mesenchymal stem cells suppresses tumor growth in mice. Conclusion The results show that this approach, if optimized, could circumvent the obstacles to efficient gene delivery encountered with current gene delivery approaches and provide an effective, nontoxic therapeutic alternative for metastatic disease.
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Affiliation(s)
- Tahir Muhammad
- College of life sciences and Bio-engineering, Beijing University of Technology, Beijing, China
| | - Ali Sakhawat
- College of life sciences and Bio-engineering, Beijing University of Technology, Beijing, China
| | - Aamir Ali Khan
- College of life sciences and Bio-engineering, Beijing University of Technology, Beijing, China
| | - Ling Ma
- College of life sciences and Bio-engineering, Beijing University of Technology, Beijing, China
| | - Ruth A Gjerset
- Torrey Pines Institute for Molecular Studies, San Diego, CA, USA
| | - Yinghui Huang
- College of life sciences and Bio-engineering, Beijing University of Technology, Beijing, China.
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137
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Langley SA, Miga KH, Karpen GH, Langley CH. Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA. eLife 2019; 8:e42989. [PMID: 31237235 PMCID: PMC6592686 DOI: 10.7554/elife.42989] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/20/2019] [Indexed: 12/22/2022] Open
Abstract
Despite critical roles in chromosome segregation and disease, the repetitive structure and vast size of centromeres and their surrounding heterochromatic regions impede studies of genomic variation. Here we report the identification of large-scale haplotypes (cenhaps) in humans that span the centromere-proximal regions of all metacentric chromosomes, including the arrays of highly repeated α-satellites on which centromeres form. Cenhaps reveal deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans. These centromere-spanning haplotypes contain variants, including large differences in α-satellite DNA content, which may influence the fidelity and bias of chromosome transmission. The discovery of cenhaps creates new opportunities to investigate their contribution to phenotypic variation, especially in meiosis and mitosis, as well as to more incisively model the unexpectedly rich evolution of these challenging genomic regions.
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Affiliation(s)
- Sasha A Langley
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Karen H Miga
- UC Santa Cruz Genomics InstituteUniversity of California, Santa CruzSanta CruzUnited States
| | - Gary H Karpen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Charles H Langley
- Department of Evolution and EcologyUniversity of California, DavisDavisUnited States
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138
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Chen H, Kichaev G, Bien SA, MacDonald JW, Wang L, Bammler TK, Auer P, Pasaniuc B, Lindström S. Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues. Hum Genet 2019; 138:1091-1104. [PMID: 31230194 DOI: 10.1007/s00439-019-02041-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of risk loci for breast and prostate cancer, only a few studies have characterized the GWAS association signals across functional genomic annotations with a particular focus on single nucleotide polymorphisms (SNPs) located in DNA regulatory elements. In this study, we investigated the enrichment pattern of GWAS signals for breast and prostate cancer in genomic functional regions located in normal tissue and cancer cell lines. We quantified the overall enrichment of SNPs with breast and prostate cancer association p values < 1 × 10-8 across regulatory categories. We then obtained annotations for DNaseI hypersensitive sites (DHS), typical enhancers, and super enhancers across multiple tissue types, to assess if significant GWAS signals were selectively enriched in annotations found in disease-related tissue. Finally, we quantified the enrichment of breast and prostate cancer SNP heritability in regulatory regions, and compared the enrichment pattern of SNP heritability with GWAS signals. DHS, typical enhancers, and super enhancers identified in the breast cancer cell line MCF-7 were observed with the highest enrichment of genome-wide significant variants for breast cancer. For prostate cancer, GWAS signals were mostly enriched in DHS and typical enhancers identified in the prostate cancer cell line LNCaP. With progressively stringent GWAS p value thresholds, an increasing trend of enrichment was observed for both diseases in DHS, typical enhancers, and super enhancers located in disease-related tissue. Results from heritability enrichment analysis supported the selective enrichment pattern of functional genomic regions in disease-related cell lines for both breast and prostate cancer. Our results suggest the importance of studying functional annotations identified in disease-related tissues when characterizing GWAS results, and further demonstrate the role of germline DNA regulatory elements from disease-related tissue in breast and prostate carcinogenesis.
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Affiliation(s)
- Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Paul Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.,Departments of Human Genetics, and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA. .,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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139
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Abstract
BACKGROUND As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that are associated with the same disease. Using Type II Diabetes (T2D) as a test case, we develop measures and methods to characterize the functional overlap of SNPs associated with the same disease across populations. RESULTS We introduce the notion of an Overlap Matrix as a general means of characterizing the functional overlap between different SNP sets at different genomic and functional granularities. Using SNP-to-gene mapping, functional annotation databases, and functional association networks, we assess the degree of functional overlap across nine populations from Asian and European ethnic origins. We further assess the generalizability of the method by applying it to a dataset for another complex disease - Prostate Cancer. Our results show that more overlap is captured as more functional data is incorporated as we go through the pipeline, starting from SNPs and ending at network overlap analyses. We hypothesize that these observed differences in the functional mechanisms of T2D across populations can also explain the common use of different prescription drugs in different populations. We show that this hypothesis is concordant with the literature on the functional mechanisms of prescription drugs. CONCLUSION Our results show that although the etiology of a complex disease can be associated with distinct processes that are affected in different populations, network-based annotations can capture more functional overlap across populations. These results support the notion that it can be useful to take ethnicity into account in making personalized treatment decisions for complex diseases.
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Affiliation(s)
- Dalia Elmansy
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106 USA
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106 USA
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140
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Lou H, Li H, Ho KJ, Cai LL, Huang AS, Shank TR, Verneris MR, Nickerson ML, Dean M, Anderson SK. The Human TET2 Gene Contains Three Distinct Promoter Regions With Differing Tissue and Developmental Specificities. Front Cell Dev Biol 2019; 7:99. [PMID: 31231651 PMCID: PMC6566030 DOI: 10.3389/fcell.2019.00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Tet methylcytosine dioxygenase 2 (TET2) is a tumor suppressor gene that is inactivated in a wide range of hematological cancers. TET2 enzymatic activity converts 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC), an essential step in DNA demethylation. Human TET2 is highly expressed in pluripotent cells and down-regulated in differentiated cells: however, transcriptional regulation of the human TET2 gene has not been investigated in detail. Here we define three promoters within a 2.5 kb region located ∼ 87 kb upstream of the first TET2 coding exon. The three promoters, designated as Pro1, Pro2, and Pro3, generate three alternative first exons, and their presence in TET2 mRNAs varies with cell type and developmental stage. In general, all three TET2 transcripts are more highly expressed in human tissues rich in hematopoietic stem cells, such as spleen and bone marrow, compared to other tissues, such as brain and kidney. Transcripts from Pro2 are expressed by a broad range of tissues and at a significantly higher level than Pro1 or Pro3 transcripts. Pro3 transcripts were highly expressed by embryoid bodies generated from the H9 ES cell line, and the major Pro3 transcript is an alternatively spliced mRNA isoform that produces a truncated TET2 protein lacking the catalytic domain. Our study demonstrates distinct tissue-specific mechanisms of TET2 transcriptional regulation during early pluripotent states and in differentiated cell types.
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Affiliation(s)
- Hong Lou
- Laboratory of Translational Genomics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, United States
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Kevin J Ho
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Luke L Cai
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Andy S Huang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Tyler R Shank
- Department of Pediatrics, Center for Cancer and Blood Disorders, University of Colorado Denver, Denver, CO, United States
| | - Michael R Verneris
- Department of Pediatrics, Center for Cancer and Blood Disorders, University of Colorado Denver, Denver, CO, United States
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD, United States
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD, United States
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
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141
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Di Meo A, Wang C, Cheng Y, Diamandis EP, Yousef GM. The miRNA-kallikrein interaction: a mosaic of epigenetic regulation in cancer. Biol Chem 2019; 399:973-982. [PMID: 29604203 DOI: 10.1515/hsz-2018-0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/26/2018] [Indexed: 12/28/2022]
Abstract
The kallikrein-related peptidases (KLKs) constitute a family of 15 highly conserved serine proteases with trypsin- and chymotrypsin-like activities. Dysregulated expression and/or aberrant activation of KLKs has been linked to various pathophysiological processes, including cancer. Many KLKs have been identified as potential cancer biomarkers. microRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by pairing to the 3' untranslated region (UTR) of complimentary mRNA targets. miRNAs are dysregulated in many cancers, including prostate, kidney and ovarian cancers. Several studies have shown that miRNAs are involved in the post-transcriptional regulation of KLKs. However, recent evidence suggests that miRNAs can also act as downstream effectors of KLKs. In this review, we provide an update on the epigenetic regulation of KLKs by miRNAs. We also present recent experimental evidence that supports the regulatory role of KLKs on miRNA networks. The potential diagnostic and therapeutic applications of miRNA-kallikrein interactions are also discussed.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Cong Wang
- Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, China
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, China
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
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142
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van Kippersluis H, Rietveld CA. Pleiotropy-robust Mendelian randomization. Int J Epidemiol 2019; 47:1279-1288. [PMID: 28338774 DOI: 10.1093/ije/dyx002] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2017] [Indexed: 01/15/2023] Open
Abstract
Background The potential of Mendelian randomization studies is rapidly expanding due to: (i) the growing power of genome-wide association study (GWAS) meta-analyses to detect genetic variants associated with several exposures; and (ii) the increasing availability of these genetic variants in large-scale surveys. However, without a proper biological understanding of the pleiotropic working of genetic variants, a fundamental assumption of Mendelian randomization (the exclusion restriction) can always be contested. Methods We build upon and synthesize recent advances in the literature on instrumental variables (IVs) estimation that test and relax the exclusion restriction. Our pleiotropy-robust Mendelian randomization (PRMR) method first estimates the degree of pleiotropy, and in turn corrects for it. If (i) a subsample exists for which the genetic variants do not affect the exposure; (ii) the selection into this subsample is not a joint consequence of the IV and the outcome; (iii) pleiotropic effects are homogeneous, PRMR obtains unbiased estimates of causal effects. Results Simulations show that existing MR methods produce biased estimators for realistic forms of pleiotropy. Under the aforementioned assumptions, PRMR produces unbiased estimators. We illustrate the practical use of PRMR by estimating the causal effect of: (i) tobacco exposure on body mass index (BMI); (ii) prostate cancer on self-reported health; and (iii) educational attainment on BMI in the UK Biobank data. Conclusions PRMR allows for instrumental variables that violate the exclusion restriction due to pleiotropy, and it corrects for pleiotropy in the estimation of the causal effect. If the degree of pleiotropy is unknown, PRMR can still be used as a sensitivity analysis.
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Affiliation(s)
- Hans van Kippersluis
- Erasmus School of Economics, Erasmus University Rotterdam, The Netherlands.,Department of Economics, Chinese University of Hong Kong, Hong Kong SAR.,Tinbergen Institute, Amsterdam, The Netherlands
| | - Cornelius A Rietveld
- Erasmus School of Economics, Erasmus University Rotterdam, The Netherlands.,Tinbergen Institute, Amsterdam, The Netherlands.,Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus University Rotterdam, The Netherlands
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143
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Crumbaker M, Wong J, Joshua AM, Spigelman AD. Outcomes of universal germline testing for men with prostate cancer in an Australian tertiary center. Asia Pac J Clin Oncol 2019; 15:257-261. [PMID: 31012270 DOI: 10.1111/ajco.13148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/02/2019] [Indexed: 11/27/2022]
Abstract
AIM The role of germline testing in prostate cancer is evolving and knowledge of an individual's genetic profile may be used to guide not only an assessment of their familial risk but also have prognostic and therapeutic implications. Although international guidelines have incorporated recommendations for germline testing in prostate cancer, there is little Australian data to guide referrals. The aim of this study is to review the frequency of relevant pathogenic mutations in an Australian center, their associated clinical factors and clinical impact. METHODS We conducted a single-center retrospective review of men with prostate cancer that undertook prospective germline testing using a targeted next generation sequencing panel. RESULTS Results for 100 men were analyzed. Median age at diagnosis was 62 years (range 43-84); 92% had metastatic disease at referral. A pathogenic mutation was confirmed in 9%, a likely pathogenic variant in 2% and a variant of uncertain significance in 15%. Age ≤60 years was associated with an increased risk for a pathogenic germline variant (P = 0.0096). Two of the nine (22%) with pathogenic variants went on to receive targeted treatment. CONCLUSIONS In this single center study, the incidence of germline mutations in genes associated with DNA-repair was consistent with rates seen previously published international series of men with metastatic disease. A pathogenic variant was only seen in one patient >60 years of age and no man referred solely on the basis of age or high-risk localized disease had a relevant finding.
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Affiliation(s)
- Megan Crumbaker
- Kinghorn Cancer Centre, St. Vincent's Hospital, Darlinghurst, NSW, Australia.,Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales, St. Vincent's Clinical School, Darlinghurst, NSW, Australia
| | - Jean Wong
- Department of Surgery, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Anthony M Joshua
- Kinghorn Cancer Centre, St. Vincent's Hospital, Darlinghurst, NSW, Australia.,Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales, St. Vincent's Clinical School, Darlinghurst, NSW, Australia
| | - Allan D Spigelman
- Kinghorn Cancer Centre, St. Vincent's Hospital, Darlinghurst, NSW, Australia.,University of New South Wales, St. Vincent's Clinical School, Darlinghurst, NSW, Australia.,Cancer Genetics Unit, St. Vincent's Hospital, Darlinghurst, NSW, Australia
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144
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Shi Z, Yu H, Wu Y, Lin X, Bao Q, Jia H, Perschon C, Duggan D, Helfand BT, Zheng SL, Xu J. Systematic evaluation of cancer-specific genetic risk score for 11 types of cancer in The Cancer Genome Atlas and Electronic Medical Records and Genomics cohorts. Cancer Med 2019; 8:3196-3205. [PMID: 30968590 PMCID: PMC6558466 DOI: 10.1002/cam4.2143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genetic risk score (GRS) is an odds ratio (OR)-weighted and population-standardized method for measuring cumulative effect of multiple risk-associated single nucleotide polymorphisms (SNPs). We hypothesize that GRS is a valid tool for risk assessment of most common cancers. METHODS Utilizing genotype and phenotype data from The Cancer Genome Atlas (TCGA) and Electronic Medical Records and Genomics (eMERGE), we tested 11 cancer-specific GRSs (bladder, breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, prostate, renal, and thyroid cancer) for association with the respective cancer type. Cancer-specific GRSs were calculated, for the first time in these cohorts, based on previously published risk-associated SNPs using the Caucasian subjects in these two cohorts. RESULTS Mean cancer-specific GRS in the population controls of eMERGE approximated the expected value of 1.00 (between 0.98 and 1.02) for all 11 types of cancer. Mean cancer-specific GRS was consistently higher in respective cancer patients than controls for all 11 types of cancer (P < 0.05). When subjects were categorized into low-, average-, and high-risk groups based on cancer-specific GRS (<0.5, 0.5-1.5, and >1.5, respectively), significant dose-response associations of higher cancer-specific GRS with higher OR of respective type of cancer were found for nine types of cancer (P-trend < 0.05). More than 64% subjects in the population controls of eMERGE can be classified as high risk for at least one type of these cancers. CONCLUSION Validity of GRS for predicting cancer risk is demonstrated for most types of cancer. If confirmed in larger studies, cancer-specific GRS may have the potential for developing personalized cancer screening strategy.
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Affiliation(s)
- Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Lin
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Quanwa Bao
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Haifei Jia
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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145
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DeRycke MS, Larson MC, Nair AA, McDonnell SK, French AJ, Tillmans LS, Riska SM, Baheti S, Fogarty ZC, Larson NB, O’Brien DR, Cheville JC, Wang L, Schaid DJ, Thibodeau SN. An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set. PLoS One 2019; 14:e0214588. [PMID: 30958860 PMCID: PMC6453468 DOI: 10.1371/journal.pone.0214588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/17/2019] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer (PrCa) is highly heritable; 284 variants have been identified to date that are associated with increased prostate cancer risk, yet few genes contributing to its development are known. Expression quantitative trait loci (eQTL) studies link variants with affected genes, helping to determine how these variants might regulate gene expression and may influence prostate cancer risk. In the current study, we performed eQTL analysis on 471 normal prostate epithelium samples and 249 PrCa-risk variants in 196 risk loci, utilizing RNA sequencing transcriptome data based on ENSEMBL gene definition and genome-wide variant data. We identified a total of 213 genes associated with known PrCa-risk variants, including 141 protein-coding genes, 16 lncRNAs, and 56 other non-coding RNA species with differential expression. Compared to our previous analysis, where RefSeq was used for gene annotation, we identified an additional 130 expressed genes associated with known PrCa-risk variants. We detected an eQTL signal for more than half (n = 102, 52%) of the 196 loci tested; 52 (51%) of which were a Group 1 signal, indicating high linkage disequilibrium (LD) between the peak eQTL variant and the PrCa-risk variant (r2>0.5) and may help explain how risk variants influence the development of prostate cancer.
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Affiliation(s)
- Melissa S. DeRycke
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Melissa C. Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Asha A. Nair
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Shannon K. McDonnell
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Amy J. French
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Lori S. Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Shaun M. Riska
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Saurabh Baheti
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Zachary C. Fogarty
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Nicholas B. Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Daniel R. O’Brien
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - John C. Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Daniel J. Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, SW, Rochester, Minnesota, United States of America
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146
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Chen B, Zhang C, Wang Z, Chen Y, Xie H, Li S, Liu X, Liu Z, Chen P. Mechanistic insights into Nav1.7-dependent regulation of rat prostate cancer cell invasiveness revealed by toxin probes and proteomic analysis. FEBS J 2019; 286:2549-2561. [PMID: 30927332 DOI: 10.1111/febs.14823] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 01/29/2019] [Accepted: 02/27/2019] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels are involved in tumor metastasis, as potentiating or attenuating their activities affects the migration and invasion process of tumor cells. In the present study, we tested the effect of two peptide toxins, JZTX-I and HNTX-III which function as Nav1.7 activator and inhibitor, respectively, on the migration and invasion ability of prostate cancer (PCa) cell line Mat-LyLu. These two peptides showed opposite effects, and subsequently a comparative proteomic analysis characterized 64 differentially expressed membrane proteins from the JZTX-I- and HNTX-III-treated groups. Among these, 15 proteins were down-regulated and 49 proteins were up-regulated in the HNTX-III group. Bioinformatic analysis showed eight proteins are cytoskeleton proteins or related regulators, which might play important roles in the metastasis of Mat-LyLu cells. The altered expressions of four of these proteins, fascin, muskelin, annexin A2, and cofilin-1, were validated by western blot analysis. Further function network analysis of these proteins revealed that the Rho family GTPases RhoA and Rac1 might be of particular importance for the rat PCa cell invasion. Pharmacological data revealed that JZTX-I and HNTX-III could modulate the Rho signaling pathway in a Nav1.7-dependent manner. In summary, this study suggests that the Nav1.7-dependent regulation of Rho GTPase activity plays a vital role in Mat-LyLu cell migration and invasion and provides new insights into the treatment of PCa.
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Affiliation(s)
- Bo Chen
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.,The Key laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Changxin Zhang
- The Key laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Zijun Wang
- The Key laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yan Chen
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Huali Xie
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Sha Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoqian Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.,The Key laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Ping Chen
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.,The Key laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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147
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Jones CC, Bradford Y, Amos CI, Blot WJ, Chanock SJ, Harris CC, Schwartz AG, Spitz MR, Wiencke JK, Wrensch MR, Wu X, Aldrich MC. Cross-Cancer Pleiotropic Associations with Lung Cancer Risk in African Americans. Cancer Epidemiol Biomarkers Prev 2019; 28:715-723. [PMID: 30894353 PMCID: PMC6449205 DOI: 10.1158/1055-9965.epi-18-0935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/02/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European-descent individuals. Yet population-specific genetic variation can occur, and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans. METHODS We conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status. RESULTS We identified three novel genomic regions significantly associated (FDR-corrected P <0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with reduced risk [OR = 0.43; 95% confidence interval (CI), 0.73-0.89], and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The minor allele at rs336958 on 5q14.3 was associated with increased lung cancer risk (OR = 1.47; 95% CI, 1.22-1.78), whereas the minor allele at rs11658063 on 17q12 was associated with reduced risk (OR = 0.80; 95% CI, 0.72-0.90). CONCLUSIONS We identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans. IMPACT Our findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuki Bradford
- School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Margaret R Spitz
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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148
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DANAU RAZVAN, BADIU DUMITRUCRISTINEL, IORDACHE PAUL, URSU RADU, RADOI VIORICA, RASCU STEFAN, RADAVOI GEORGEDANIEL, SIMA CRISTIANSORIN, TOMA CRISTIAN, BRATICEVICI BOGDAN, MANDU MIHAELA, GRIGOREAN TITUSVALENTIN, JINGA VIOREL. Genetic Risk Score for Prostate Cancer in the Romanian Population. ROMANIAN BIOTECHNOLOGICAL LETTERS 2019. [DOI: 10.25083/rbl/24.1/100.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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149
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Panigrahi GK, Praharaj PP, Kittaka H, Mridha AR, Black OM, Singh R, Mercer R, van Bokhoven A, Torkko KC, Agarwal C, Agarwal R, Abd Elmageed ZY, Yadav H, Mishra SK, Deep G. Exosome proteomic analyses identify inflammatory phenotype and novel biomarkers in African American prostate cancer patients. Cancer Med 2019; 8:1110-1123. [PMID: 30623593 PMCID: PMC6434210 DOI: 10.1002/cam4.1885] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 12/27/2022] Open
Abstract
African American men face a stark prostate cancer (PCa)-related health disparity, with the highest incidence and mortality rates compared to other races. Additional and innovative measures are warranted to reduce this health disparity. Here, we focused on the identification of a novel serum exosome-based "protein signature" for potential use in the early detection and better prognosis of PCa in African American men. Nanoparticle tracking analyses showed that compared to healthy individuals, exosome concentration (number/ml) was increased by ~3.2-fold (P ˂ 0.05) in the sera of African American men with PCa. Mass spectrometry-based proteomic analysis of serum exosomes identified seven unique and fifty-five overlapping proteins (up- or downregulated) in African Americans with PCa compared to healthy African Americans. Furthermore, ingenuity pathway analyses identified the inflammatory acute-phase response signaling as the top pathway associated with proteins loaded in exosomes from African American PCa patients. Interestingly, African American PCa E006AA-hT cells secreted exosomes strongly induced a proinflammatory M2-phenotype in macrophages and showed calcium response on sensory neurons, suggesting a neuroinflammatory response. Additionally, proteomic analyses showed that the protein Isoform 2 of Filamin A has higher loading (2.6-fold) in exosomes from African Americans with PCa, but a lesser loading (0.6-fold) was observed in exosomes from Caucasian men with PCa compared to race-matched healthy individuals. Interestingly, TCGA and Taylor's dataset as well as IHC analyses of PCa tissue showed a lower Filamin A expression in tissues of PCa patients compared with normal subjects. Overall, these results support the usefulness of serum exosomes to noninvasively detect inflammatory phenotype and to discover novel biomarkers associated with PCa in African American men.
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Affiliation(s)
- Gati K Panigrahi
- Cancer Biology Department, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Prakash P Praharaj
- Cancer Biology Department, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Hiroki Kittaka
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, North Carolina
| | - Asit R Mridha
- Cancer Biology Department, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Olen M Black
- Cancer Biology Department, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Rakesh Singh
- Translational Science Laboratory, College of Medicine, Florida State University, Tallahassee, Florida
| | - Roger Mercer
- Translational Science Laboratory, College of Medicine, Florida State University, Tallahassee, Florida
| | - Adrie van Bokhoven
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kathleen C Torkko
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Chapla Agarwal
- School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Rajesh Agarwal
- School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Zakaria Y Abd Elmageed
- Department of Pharmaceutical Sciences, Texas A&M Rangel College of Pharmacy, College Station, Texas
| | - Hariom Yadav
- Department of Internal Medicine-Molecular Medicine and Department of Microbiology and Immunology, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Santosh K Mishra
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, North Carolina
| | - Gagan Deep
- Cancer Biology Department, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.,Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina.,Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina
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150
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Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E. An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Genome Res 2019; 29:223-235. [PMID: 30606742 PMCID: PMC6360806 DOI: 10.1101/gr.230243.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/13/2018] [Indexed: 01/10/2023]
Abstract
The aberrant activities of transcription factors such as the androgen receptor (AR) underpin prostate cancer development. While the AR cis-regulation has been extensively studied in prostate cancer, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited. In this paper, we propose a novel framework to profile long-range chromatin interactions associated with AR and its collaborative transcription factor, erythroblast transformation-specific related gene (ERG), using chromatin interaction analysis by paired-end tag (ChIA-PET). We identified ERG-associated long-range chromatin interactions as a cooperative component in the AR-associated chromatin interactome, acting in concert to achieve coordinated regulation of a subset of AR target genes. Through multifaceted functional data analysis, we found that AR-ERG interaction hub regions are characterized by distinct functional signatures, including bidirectional transcription and cotranscription factor binding. In addition, cancer-associated long noncoding RNAs were found to be connected near protein-coding genes through AR-ERG looping. Finally, we found strong enrichment of prostate cancer genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) at AR-ERG co-binding sites participating in chromatin interactions and gene regulation, suggesting GWAS target genes identified from chromatin looping data provide more biologically relevant findings than using the nearest gene approach. Taken together, our results revealed an AR-ERG-centric higher-order chromatin structure that drives coordinated gene expression in prostate cancer progression and the identification of potential target genes for therapeutic intervention.
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Affiliation(s)
- Zhizhuo Zhang
- School of Computing, National University of Singapore, Singapore 117417.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Shreyas Lingadahalli
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Zikai Chen
- Genome Institute of Singapore, Singapore 138672.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Mei Hui Liu
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Nicola Rinaldi
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Guoliang Li
- Genome Institute of Singapore, Singapore 138672.,National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | | | | | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Si Kee Tan
- Genome Institute of Singapore, Singapore 138672
| | - Xiaoan Ruan
- Genome Institute of Singapore, Singapore 138672
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672
| | - Wing-Kin Sung
- School of Computing, National University of Singapore, Singapore 117417.,Genome Institute of Singapore, Singapore 138672
| | - Edwin Cheung
- Genome Institute of Singapore, Singapore 138672.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
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